Markers + reference

Celastrus

12 species · Celastraceae · Celastrales

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Species 12
Genome length 156–157 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 411 0.0471 0.99 82.2 yes View details
rps16-trnQ-UUG LSC 964 0.0188 0.99 69.6 yes View details
trnG-UCC-trnR-UCU LSC 368 0.0411 0.97 69.6 yes View details
petN-psbM LSC 812 0.0192 0.99 63.5 yes View details
psbZ-trnG-GCC LSC 724 0.0253 0.96 67.0 yes View details
ndhC-trnV-UAC LSC 467 0.0158 0.97 58.9 yes View details
trnM-CAU-atpE LSC 281 0.0416 0.98 72.1 yes View details
ycf4-cemA LSC 558 0.0239 1.00 70.1 yes View details
psbE-petL LSC 1116 0.0153 0.99 61.1 yes View details
rpl16 LSC 1505 0.0139 0.98 58.2 yes View details
ycf1 IRb 952 0.0065 1.00 43.7 no View details
ycf1 SSC 5556 0.0148 1.00 52.3 yes View details
atpA-atpF LSC 65 0.0806 0.92 74.2 yes View details
rps19-trnH-GUG IRa 30 0.0485 1.00 73.8 no View details
trnF-GAA-ndhJ LSC 790 0.0195 0.99 72.9 yes View details
psbM-trnD-GUC LSC 626 0.0143 1.00 70.6 yes View details
atpH-atpI LSC 1221 0.0123 1.00 69.2 yes View details
ycf3-trnS-GGA LSC 878 0.0158 0.98 68.1 yes View details
rpl22-rps19 LSC 81 0.0389 0.99 67.4 yes View details
clpP-psbB LSC 445 0.0098 0.97 67.1 yes View details
trnK-UUU-rps16 LSC 609 0.0195 0.97 65.9 yes View details
ccsA-ndhD SSC 251 0.0312 1.00 65.7 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 521–576 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 535–590 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 534–589 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 536–591 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT GCGCTAACCTTGGTATGGAA 541–596 1.000 90.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGGGGTTTTTACGCAATTC 690–723 1.000 79.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGGGGTTTTTACGCAATTC 689–722 1.000 79.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGGGTTTTTACGCAATTCT 689–722 1.000 79.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGGGTTTTTACGCAATTCT 688–721 1.000 79.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TCGGGGTTTTTACGCAATTC 676–709 1.000 77.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG GAGGTTCGAATCCTTCCGTC 1080–1135 1.000 87.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG AATAGAATATGGGGCGTGGC 1137–1192 1.000 86.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCGATCGAACATCAATTGCA GAGGTTCGAATCCTTCCGTC 1067–1122 1.000 84.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA GAGGTTCGAATCCTTCCGTC 1083–1138 0.917 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA AATAGAATATGGGGCGTGGC 1140–1195 0.917 81.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 413–465 1.000 52.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGTCCTATCCATTAGACAATG 416–468 1.000 52.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AACGCCGACTATAACCCCTA TGTCCTATCCATTAGACAATG 432–484 1.000 52.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCGACTATAACCCCTAGCCT TGTCCTATCCATTAGACAATG 428–480 1.000 52.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGTCCTATCCATTAGACAATG 417–469 1.000 52.0
atpA-atpF_p1 atpA-atpF ACTAATTTCGTCGGCTCGAA GGCATCTTTGGGACGATGAA 124–136 1.000 84.9
atpA-atpF_p2 atpA-atpF ACTAATTTCGTCGGCTCGAA ATTGGCATCTTTGGGACGAT 127–139 1.000 83.3
atpA-atpF_p3 atpA-atpF ACTAATTTCGTCGGCTCGAA TTGGCATCTTTGGGACGATG 126–138 1.000 82.6
atpA-atpF_p4 atpA-atpF ACTAATTTCGTCGGCTCGAA ACAAGCCCTACAAGAAGCTC 206–218 1.000 82.3
atpA-atpF_p5 atpA-atpF AATTTCGTCGGCTCGAATGG GGCATCTTTGGGACGATGAA 121–133 1.000 82.1
atpH-atpI_p1 atpH-atpI AATCACAGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1310–1348 1.000 82.2
atpH-atpI_p2 atpH-atpI ATCACAGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1309–1347 1.000 82.1
atpH-atpI_p3 atpH-atpI AATCACAGAAGCGGCAGAAA TAGGTGAATCCATGGAGGGT 1283–1321 1.000 81.8
atpH-atpI_p4 atpH-atpI ATCACAGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1282–1320 1.000 81.7
atpH-atpI_p5 atpH-atpI AATAGAAGCAAGACCGACGG TTTTTGCAACTTTAGCCGCG 1343–1381 1.000 80.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Celastrus angulatus OR726623.1 155995 View on NCBI ↗
Celastrus gemmatus NC_065717.1 156514 View on NCBI ↗
Celastrus hindsii OR726625.1 157323 View on NCBI ↗
Celastrus hirsutus OR726626.1 156368 View on NCBI ↗
Celastrus kusanoi NC_066674.1 156457 View on NCBI ↗
Celastrus monospermus OR726627.1 156001 View on NCBI ↗
Celastrus orbiculatus OR726628.1 156707 View on NCBI ↗
Celastrus paniculatus NC_061667.1 157119 View on NCBI ↗
Celastrus rugosus OR726629.1 156896 View on NCBI ↗
Celastrus stylosus NC_065710.1 156458 View on NCBI ↗
Celastrus tonkinensis OR726631.1 157342 View on NCBI ↗
Celastrus vaniotii OR726632.1 157194 View on NCBI ↗